[A multi-molecular predictive model for lymph node metastasis in papillary thyroid carcinoma based on machine...

Accurate preoperative evaluation of lymph node metastasis (LNM) status in patients with papillary thyroid carcinoma (PTC) is essential for the development of individualized diagnosis and treatment strategies; however, the predictive performance of current clinical approaches remains limited. This study aims to identify key molecular biomarkers associated with LNM in PTC, construct LNM-risk prediction models using machine learning (ML) algorithms, and assess their potential value in supporting clinical decision-making.

Transcriptomic data from 507 PTC patients were obtained from The Cancer Genome Atlas (TCGA). After rigorous quality control, 50 patients with unknown lymph node status (N-stage) were excluded, leaving 457 eligible patients [229 with no LNM (N0) and 228 with LNM (N1)]. Patients were randomly stratified into a training set (n=321) and a validation set (n=136) at a 7꞉3 ratio. Four independent analytical methods-Differential Expression analysis based on the Negative Binomial distribution (DESeq2), Empirical analysis of Digital Gene Expression in R (edgeR), Linear Models for Microarray Analysis (Limma), and Weighted Gene Co-expression Network Analysis (WGCNA)-were applied to identify LNM-associated candidate gene sets. Core genes were further selected from each set using least absolute shrinkage and selection operator (LASSO) regression, and multivariate logistic regression models were built on the training cohort. Model performance and generalizability were evaluated using receiver operating characteristic (ROC) curves, confusion matrices, calibration curves (CC), decision curve analysis (DCA), and ML cross-validation across six algorithms: Generalized linear model (GLM), random forest (RF), extreme gradient boosting (XGBoost), artificial neural network (ANN), support vector machine (SVM), and naive Bayes model (NBM).

EdgeR combined with LASSO regression identified 11 signature genes associated with LNM in PTC: PI15, IL11, PLA2G5, LY6G6C, FAM178B, MUC21, FN1, PDZK1IP1, STAC2, TMPRSS4, and WARS1P1. The multivariate logistic model constructed from these genes (Model 2) showed the best predictive performance. In the training set, the area under the ROC curve (AUC) was 0.802, with a sensitivity of 0.771 and specificity of 0.797. In the validation set, the AUC was 0.793, with a sensitivity of 0.773 and specificity of 0.634. Sex-stratified analyses confirmed stable performance in the overall cohort (AUC=0.780), females (AUC=0.775), and males (AUC=0.807). ML cross-validation demonstrated that Model 2 achieved superior and well-balanced predictive performance across all 6 ML algorithms. CC analysis demonstrated strong agreement between predicted and observed LNM probabilities (Hosmer-Lemeshow goodness-of-fit test: P_training=0.851, P_validation=0.842). DCA revealed significant net clinical benefit in the training cohort across risk thresholds from 0.1 to 0.75, whereas validation-cohort benefit was present only at low thresholds (<0.3) and declined with increasing thresholds. Expression levels of all 11 signature genes were significantly higher in the N1 group than in the N0 group (all P<0.001).

The optimized multi-molecular logistic regression model (Model 2) built on 11 signature genes can effectively predict lymph node metastasis risk in PTC patients, demonstrating robust cross-sex stability, strong compatibility across multiple ML algorithms, and potential clinical utility as a preoperative decision-support tool for lymph node status assessment and personalized treatment planning.